10-105076813-G-T

Variant names:

• chr10-105076813-G-T
• rs703460
• NM_014978.3:c.1029-12962G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014978.3(SORCS3):​c.1029-12962G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,096 control chromosomes in the GnomAD database, including 36,333 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (36333 hom., cov: 32)
• Consequence: SORCS3 NM_014978.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 1 publications found

Genes affected

SORCS3 (HGNC:16699): (sortilin related VPS10 domain containing receptor 3) This gene encodes a type-I receptor transmembrane protein that is a member of the vacuolar protein sorting 10 receptor family. Proteins of this family are defined by a vacuolar protein sorting 10 domain at the N-terminus. The N-terminal segment of this domain has a consensus motif for proprotein convertase processing, and the C-terminal segment of this domain is characterized by ten conserved cysteine residues. The vacuolar protein sorting 10 domain is followed by a leucine-rich segment, a transmembrane domain, and a short C-terminal cytoplasmic domain that interacts with adaptor molecules. The transcript is expressed at high levels in the brain, and candidate gene studies suggest that genetic variation in this gene is associated with Alzheimer's disease. Consistent with this observation, knockdown of the gene in cell culture results in an increase in amyloid precursor protein processing. [provided by RefSeq, Dec 2014]

SORCS3 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014978.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SORCS3	NM_014978.3	MANE Select	c.1029-12962G>T		intron	N/A	NP_055793.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SORCS3	ENST00000369701.8	TSL:1 MANE Select	c.1029-12962G>T		intron	N/A	ENSP00000358715.3

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104731 AN: 151978 Hom.: 36313 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.694

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.689 AC: 104798 AN: 152096 Hom.: 36333 Cov.: 32 AF XY: 0.692 AC XY: 51459 AN XY: 74352

African (AFR) AF: 0.705 AC: 29252 AN: 41484

American (AMR) AF: 0.612 AC: 9352 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2435 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4319 AN: 5168

South Asian (SAS) AF: 0.639 AC: 3077 AN: 4818

European-Finnish (FIN) AF: 0.795 AC: 8409 AN: 10582

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45759 AN: 67978

Other (OTH) AF: 0.689 AC: 1457 AN: 2116

Alfa AF: 0.675 Hom.: 5108

Bravo AF: 0.680

Asia WGS AF: 0.677 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.80
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs703460; hg19: chr10-106836571;